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scrm is a coalescence simulator for the evolution of biological sequences. It is available as a command line program at scrm.github.io.
This R package contains a copy scrm, packaged for convenient usage in R.
It is recommended to use the current CRAN version. It can be installed from within R using
install.packages('scrm')Use the function scrm::scrm() to call scrm:
library('scrm')
sum_stats <- scrm('5 1 -r 10 100 -t 5 -oSFS')scrm::scrm() is explained in its R help page help('scrm').vignette('scrm-Arguments').Please cite the following article when using scrm in a publication:
Paul R. Staab, Sha Zhu, Dirk Metzler and Gerton Lunter. scrm: efficiently simulating long sequences using the approximated coalescent with recombination. Bioinformatics (2015) 31 (10): 1680-1682. doi:10.1093/bioinformatics/btu861.
Please report any problems via the issue tracker or via email to develop (at) paulstaab (dot) de.
Please include the version you are using and the exact command that causes the problem including seed (if applicable) in the report. Also, feel free to suggest features there.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.